Liver is present in all vertebrates and central to many physiological processes including processing of nutrients from ingested food, plasma protein synthesis, hormone production, and detoxification. However, its evolutionary origin remains open to date. Liver is also the principal organ of acute phase response (APR) but when the vertebrate-like APR regulatory network emerges during the chordate evolution is unknown. By combining global genome survey and qRT-PCR data sets, here, we clearly demonstrate the presence of the 58 vertebrate (zebrafish) liver-specific genes in amphioxus (hepatic cecum-specific genes) that are expressed in a tissue-specific manner in the hepatic cecum, the homolog of liver. Among these 58 hepatic cecum-specific genes, 52 genes respond to lipopolysaccharide challenge, which show similar expression profiles in both zebrafish and amphioxus. In addition, searching for binding sites for HNF and APR-associated transcription factors in promoter sequences for all the 58 hepatic cecum-specific genes and the 52 APR-related genes suggests that both HNF factors and APR-associated transcription factors in amphioxus form regulatory networks similar to those observed in zebrafish, regulating the hepatic cecum-specific genes and APR-related genes, respectively, via binding to their binding sites in the promoter regions. These similarities in liver/hepatic cecum-specific genes, APR, and regulatory networks between amphioxus and zebrafish supports the idea that hepatic cecum in amphioxus is the "pre-hepatic" organ homologous to vertebrate liver and acts as an immunological organ, playing an important role in APR.